[med-svn] r2154 - in trunk/packages/fastdnaml/trunk: . debian debian/patches debian/tests
plessy at alioth.debian.org
plessy at alioth.debian.org
Sun Jul 6 01:11:54 UTC 2008
Author: plessy
Date: 2008-07-06 01:11:53 +0000 (Sun, 06 Jul 2008)
New Revision: 2154
Added:
trunk/packages/fastdnaml/trunk/Makefile
trunk/packages/fastdnaml/trunk/debian/fastDNAml.1
trunk/packages/fastdnaml/trunk/debian/tests/
trunk/packages/fastdnaml/trunk/debian/tests/Makefile
trunk/packages/fastdnaml/trunk/debian/tests/fastdnaml.data
trunk/packages/fastdnaml/trunk/fastDNAml-util
trunk/packages/fastdnaml/trunk/fastdnaml-1.2.1.announce
Removed:
trunk/packages/fastdnaml/trunk/debian/patches/Makefile.diff
trunk/packages/fastdnaml/trunk/debian/patches/fastDNAml-util.diff
trunk/packages/fastdnaml/trunk/debian/patches/fastDNAml.1.diff
trunk/packages/fastdnaml/trunk/debian/patches/fastdnaml-1.2.1.announce.diff
trunk/packages/fastdnaml/trunk/debian/patches/tests.patch
Modified:
trunk/packages/fastdnaml/trunk/debian/
trunk/packages/fastdnaml/trunk/debian/changelog
trunk/packages/fastdnaml/trunk/debian/control
trunk/packages/fastdnaml/trunk/debian/examples
trunk/packages/fastdnaml/trunk/debian/manpages
trunk/packages/fastdnaml/trunk/debian/patches/scripts.patch
trunk/packages/fastdnaml/trunk/debian/patches/series
Log:
Maintainence release.
* debian/control:
- Added myself to the uploaders field.
- Removed the [Biology] tag from the short description.
* debian/patches/{fast*,Makefile.diff,tests.patch} shipped some plain files
as patches. I created the files properly and deleted the corresopnding
patches.
* Annotated debian/patches/scripts.patch according to Debian-Med's policy.
* Corrected a link in debian/fastDNAml.1.
Added: trunk/packages/fastdnaml/trunk/Makefile
===================================================================
--- trunk/packages/fastdnaml/trunk/Makefile (rev 0)
+++ trunk/packages/fastdnaml/trunk/Makefile 2008-07-06 01:11:53 UTC (rev 2154)
@@ -0,0 +1,13 @@
+all: fastDNAml
+
+fastDNAml:
+ (cd source; cc ${CFLAGS} fastDNAml.c -o fastDNAml -lm)
+
+install:
+ install -m0755 source/fastDNAml fastDNAml-util ${DESTDIR}/usr/bin
+ install -m0755 scripts/* ${DESTDIR}/usr/lib/fastdnaml/bin
+
+clean:
+ -(cd source; rm -f *.o fastDNAml)
+ -(cd tests.fastDNAml; $(MAKE) clean)
+ -rm -f checkpoint.*
Property changes on: trunk/packages/fastdnaml/trunk/debian
___________________________________________________________________
Name: mergeWithUpstream
+ 1
Modified: trunk/packages/fastdnaml/trunk/debian/changelog
===================================================================
--- trunk/packages/fastdnaml/trunk/debian/changelog 2008-07-06 00:41:27 UTC (rev 2153)
+++ trunk/packages/fastdnaml/trunk/debian/changelog 2008-07-06 01:11:53 UTC (rev 2154)
@@ -1,8 +1,16 @@
-fastdnaml (1.2.2-8) UNRELEASED; urgency=low
+fastdnaml (1.2.2-8) unstable; urgency=low
* Changed the doc-base section according to the new policy.
+ * debian/control:
+ - Added myself to the uploaders field.
+ - Removed the [Biology] tag from the short description.
+ * debian/patches/{fast*,Makefile.diff,tests.patch} shipped some plain files
+ as patches. I created the files properly and deleted the corresopnding
+ patches.
+ * Annotated debian/patches/scripts.patch according to Debian-Med's policy.
+ * Corrected a link in debian/fastDNAml.1.
- -- Charles Plessy <charles-debian-nospam at plessy.org> Sat, 22 Mar 2008 11:39:35 +0900
+ -- Charles Plessy <plessy at debian.org> Sun, 06 Jul 2008 18:42:52 +0900
fastdnaml (1.2.2-7) unstable; urgency=low
Modified: trunk/packages/fastdnaml/trunk/debian/control
===================================================================
--- trunk/packages/fastdnaml/trunk/debian/control 2008-07-06 00:41:27 UTC (rev 2153)
+++ trunk/packages/fastdnaml/trunk/debian/control 2008-07-06 01:11:53 UTC (rev 2154)
@@ -3,7 +3,7 @@
Priority: optional
Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
DM-Upload-Allowed: yes
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders: Andreas Tille <tille at debian.org>, Charles Plessy <plessy at debian.org>
Build-Depends: cdbs (>= 0.4.23-1.1), quilt, debhelper (>= 5)
Standards-Version: 3.7.3
Homepage: http://web.archive.org/web/20061017161001/http://geta.life.uiuc.edu/~gary/programs/fastDNAml.html
@@ -14,7 +14,7 @@
Architecture: any
Depends: ${shlibs:Depends}
Suggests: phylip
-Description: [Biology] Tool for construction of phylogenetic trees of DNA sequences
+Description: Tool for construction of phylogenetic trees of DNA sequences
fastDNAml is a program derived from Joseph Felsenstein's version 3.3 DNAML
(part of his PHYLIP package). Users should consult the documentation for
DNAML before using this program.
Modified: trunk/packages/fastdnaml/trunk/debian/examples
===================================================================
--- trunk/packages/fastdnaml/trunk/debian/examples 2008-07-06 00:41:27 UTC (rev 2153)
+++ trunk/packages/fastdnaml/trunk/debian/examples 2008-07-06 01:11:53 UTC (rev 2154)
@@ -1,2 +1,2 @@
testdata/*
-tests
+debian/tests
Added: trunk/packages/fastdnaml/trunk/debian/fastDNAml.1
===================================================================
--- trunk/packages/fastdnaml/trunk/debian/fastDNAml.1 (rev 0)
+++ trunk/packages/fastdnaml/trunk/debian/fastDNAml.1 2008-07-06 01:11:53 UTC (rev 2154)
@@ -0,0 +1,41 @@
+.TH fastDNAml 1
+.\" NAME should be all caps, SECTION should be 1-8, maybe w/ subsection
+.\" other parms are allowed: see man(7), man(1)
+.SH NAME
+fastDNAml \- DNA Maximum Likelihood program
+.SH SYNOPSIS
+.B fastDNAml
+.I "< infile > outfile"
+.PP
+.B fastDNAml-util
+.I " utility"
+.SH "DESCRIPTION"
+.B fastDNAml
+is derived from Joseph Felsenstein's version 3.3 DNAML.
+.PP
+This manual page documents briefly the
+.B fastDNAml
+and
+.B fastDNAml-util
+commands.
+This manual page was written for the Debian GNU/Linux distribution
+because the original program does not have a manual page.
+Instead, it has documentation in text format. See below.
+.SH OPTIONS
+No options on the command line. They are supplied in the input file.
+Some of the utilities scripts may help you to add options. Type
+.B fastDNAml-util
+alone to get the list of utilities.
+For instance,
+.B fastDNAml-util global
+will add the 'G' (for global) option to its standard input and will send
+it to standard output. See examples in
+.IR /usr/share/doc/fastdnaml/examples/tests/Makefile.
+.SH "SEE ALSO"
+The programs are documented fully in
+.IR /usr/share/doc/fastdnaml.
+Since fastDNAml is based on Phylip's DNAML, reading the documentation of
+Phylip is recommended, too.
+.SH AUTHOR
+This manual page was written by Stephane Bortzmeyer <bortzmeyer at debian.org>,
+for the Debian GNU/Linux system (but may be used by others).
Modified: trunk/packages/fastdnaml/trunk/debian/manpages
===================================================================
--- trunk/packages/fastdnaml/trunk/debian/manpages 2008-07-06 00:41:27 UTC (rev 2153)
+++ trunk/packages/fastdnaml/trunk/debian/manpages 2008-07-06 01:11:53 UTC (rev 2154)
@@ -1 +1 @@
-fastDNAml.1
+debian/fastDNAml.1
Deleted: trunk/packages/fastdnaml/trunk/debian/patches/Makefile.diff
===================================================================
--- trunk/packages/fastdnaml/trunk/debian/patches/Makefile.diff 2008-07-06 00:41:27 UTC (rev 2153)
+++ trunk/packages/fastdnaml/trunk/debian/patches/Makefile.diff 2008-07-06 01:11:53 UTC (rev 2154)
@@ -1,16 +0,0 @@
---- /dev/null
-+++ fastdnaml-1.2.2/Makefile
-@@ -0,0 +1,13 @@
-+all: fastDNAml
-+
-+fastDNAml:
-+ (cd source; cc ${CFLAGS} fastDNAml.c -o fastDNAml -lm)
-+
-+install:
-+ install -m0755 source/fastDNAml fastDNAml-util ${DESTDIR}/usr/bin
-+ install -m0755 scripts/* ${DESTDIR}/usr/lib/fastdnaml/bin
-+
-+clean:
-+ -(cd source; rm -f *.o fastDNAml)
-+ -(cd tests.fastDNAml; $(MAKE) clean)
-+ -rm -f checkpoint.*
Deleted: trunk/packages/fastdnaml/trunk/debian/patches/fastDNAml-util.diff
===================================================================
--- trunk/packages/fastdnaml/trunk/debian/patches/fastDNAml-util.diff 2008-07-06 00:41:27 UTC (rev 2153)
+++ trunk/packages/fastdnaml/trunk/debian/patches/fastDNAml-util.diff 2008-07-06 01:11:53 UTC (rev 2154)
@@ -1,27 +0,0 @@
---- /dev/null
-+++ fastdnaml-1.2.2/fastDNAml-util
-@@ -0,0 +1,24 @@
-+#!/bin/sh
-+
-+BINDIR=/usr/lib/fastdnaml/bin
-+
-+if [ $# -lt 1 ] ; then
-+ echo "Usage: $0 <utility>" 1>&2
-+ echo " Existing utilities are:"
-+ ls ${BINDIR}
-+ exit 1
-+fi
-+
-+WRAPPER=$0
-+PROGRAM=$1
-+shift
-+ARGS=$*
-+
-+if [ -x ${BINDIR}/${PROGRAM} ]; then
-+ exec ${BINDIR}/${PROGRAM} ${ARGS}
-+else
-+ echo "Usage: utility ${PROGRAM} does not exist in fastDNAml"
-+ echo " Existing utilities are:"
-+ ls ${BINDIR}
-+ exit 1
-+fi
Deleted: trunk/packages/fastdnaml/trunk/debian/patches/fastDNAml.1.diff
===================================================================
--- trunk/packages/fastdnaml/trunk/debian/patches/fastDNAml.1.diff 2008-07-06 00:41:27 UTC (rev 2153)
+++ trunk/packages/fastdnaml/trunk/debian/patches/fastDNAml.1.diff 2008-07-06 01:11:53 UTC (rev 2154)
@@ -1,44 +0,0 @@
---- /dev/null
-+++ fastdnaml-1.2.2/fastDNAml.1
-@@ -0,0 +1,41 @@
-+.TH fastDNAml 1
-+.\" NAME should be all caps, SECTION should be 1-8, maybe w/ subsection
-+.\" other parms are allowed: see man(7), man(1)
-+.SH NAME
-+fastDNAml \- DNA Maximum Likelihood program
-+.SH SYNOPSIS
-+.B fastDNAml
-+.I "< infile > outfile"
-+.PP
-+.B fastDNAml-util
-+.I " utility"
-+.SH "DESCRIPTION"
-+.B fastDNAml
-+is derived from Joseph Felsenstein's version 3.3 DNAML.
-+.PP
-+This manual page documents briefly the
-+.B fastDNAml
-+and
-+.B fastDNAml-util
-+commands.
-+This manual page was written for the Debian GNU/Linux distribution
-+because the original program does not have a manual page.
-+Instead, it has documentation in text format. See below.
-+.SH OPTIONS
-+No options on the command line. They are supplied in the input file.
-+Some of the utilities scripts may help you to add options. Type
-+.B fastDNAml-util
-+alone to get the list of utilities.
-+For instance,
-+.B fastDNAml-util global
-+will add the 'G' (for global) option to its standard input and will send
-+it to standard output. See examples in
-+.IR /usr/share/doc/fastdnaml/tests/Makefile.
-+.SH "SEE ALSO"
-+The programs are documented fully in
-+.IR /usr/share/doc/fastdnaml.
-+Since fastDNAml is based on Phylip's DNAML, reading the documentation of
-+Phylip is recommended, too.
-+.SH AUTHOR
-+This manual page was written by Stephane Bortzmeyer <bortzmeyer at debian.org>,
-+for the Debian GNU/Linux system (but may be used by others).
Deleted: trunk/packages/fastdnaml/trunk/debian/patches/fastdnaml-1.2.1.announce.diff
===================================================================
--- trunk/packages/fastdnaml/trunk/debian/patches/fastdnaml-1.2.1.announce.diff 2008-07-06 00:41:27 UTC (rev 2153)
+++ trunk/packages/fastdnaml/trunk/debian/patches/fastdnaml-1.2.1.announce.diff 2008-07-06 01:11:53 UTC (rev 2154)
@@ -1,7 +0,0 @@
---- /dev/null
-+++ fastdnaml-1.2.2/fastdnaml-1.2.1.announce
-@@ -0,0 +1,4 @@
-+Warning: fastDNAml 1.2 changed drastically its user interface. Many utilities
-+like "frequencies" are no longer necessary. Many default options changed.
-+See the documentation or the Makefile in the tests directory.
-+
Modified: trunk/packages/fastdnaml/trunk/debian/patches/scripts.patch
===================================================================
--- trunk/packages/fastdnaml/trunk/debian/patches/scripts.patch 2008-07-06 00:41:27 UTC (rev 2153)
+++ trunk/packages/fastdnaml/trunk/debian/patches/scripts.patch 2008-07-06 01:11:53 UTC (rev 2154)
@@ -1,3 +1,9 @@
+Author: unknown
+Forwarded: No
+ fastDNAml is not maintained upstream anymore.
+Description: corrects extra spaces, a typo causing a syntax error, and adds a
+ path to the Debian-specific location of some files.
+License: see debian/copyright
--- fastdnaml-1.2.2.orig/scripts/fastDNAml_boot
+++ fastdnaml-1.2.2/scripts/fastDNAml_boot
@@ -1,5 +1,8 @@
Modified: trunk/packages/fastdnaml/trunk/debian/patches/series
===================================================================
--- trunk/packages/fastdnaml/trunk/debian/patches/series 2008-07-06 00:41:27 UTC (rev 2153)
+++ trunk/packages/fastdnaml/trunk/debian/patches/series 2008-07-06 01:11:53 UTC (rev 2154)
@@ -1,6 +1 @@
-fastdnaml-1.2.1.announce.diff
-fastDNAml.1.diff
-fastDNAml-util.diff
-Makefile.diff
scripts.patch
-tests.patch
Deleted: trunk/packages/fastdnaml/trunk/debian/patches/tests.patch
===================================================================
--- trunk/packages/fastdnaml/trunk/debian/patches/tests.patch 2008-07-06 00:41:27 UTC (rev 2153)
+++ trunk/packages/fastdnaml/trunk/debian/patches/tests.patch 2008-07-06 01:11:53 UTC (rev 2154)
@@ -1,48 +0,0 @@
---- /dev/null
-+++ fastDNAml_1.2.2/tests/Makefile
-@@ -0,0 +1,22 @@
-+# Samples and tests by Catherine Letondal <letondal at pasteur.fr>
-+
-+
-+test: fastDNAml fastDNAml_boot
-+
-+oldfastDNAml:
-+ cat fastdnaml.data | fastDNAml-util frequencies | fastDNAml-util printdata | fastDNAml-util treefile | fastDNAml > fastdnaml.out ; fastDNAml-util clean_checkpoints
-+
-+fastDNAml:
-+ cat fastdnaml.data | fastDNAml-util printdata | fastDNAml > fastdnaml.out ; fastDNAml-util clean_checkpoints
-+
-+fastDNAml_boot:
-+ cat fastdnaml.data | fastDNAml-util printdata > fastdnaml.data.tmp; fastDNAml-util fastDNAml_boot -out -boots 2 -max 2 fastdnaml.data.tmp 2
-+
-+clean:
-+ rm -f *.tmp*
-+ rm -f *.out
-+ rm -f treefile*
-+ rm -f checkpoint.*
-+
-+
-+
---- /dev/null
-+++ fastDNAml_1.2.2/tests/fastdnaml.data
-@@ -0,0 +1,20 @@
-+ 4 232
-+Bovine CCAAAAACCC CTTGTCCCCC CTCCCCTTTA AAACCCCCAA AAAACCCTTA AACCCCAAAA
-+Mouse CCAAAAAAAA AAAACTCCAA AACCCCCCCA CCCCCCCCTA AGGTCCCCCA AACCCAGGGG
-+Gorilla CCCCAAATTT TTTATCATAA AACCCCCCCA AAACCCCCCA ACCCAAACCA AACCCTTTTT
-+Human CCCCAAACCC TCCACCATCC AACCCCCCCA AAACTTTTCA ACCTAAACCA AATTTTTTTT
-+
-+ AATAACACCC ACTACCCAAA AAAATATTCC CAAACACTCC AAAAAATACC CCCCCAACCC
-+ AATAATACCC CCAACCCAAA AAAACAAACC TAAATACCTC AAAAAACACC CCCCCAATCC
-+ GACCCCCCCC CTCGCCCGGA AAAACAAATT CAAACACCTC AAAAAACACC CCTTCAGCTC
-+ AACCCTCCCC CCAACCCGGA AAGGCAAATT CAAACACCTC AAAGGGCACC CCTCCAACCC
-+
-+ GCCCACCCCC CAACCCCCCC CCCCTTGCCC CACGGTCACC CAACCCCTTT CTTTCACCCA
-+ ACCCGCCCCC CAACCCCTTT TTCCCCGCCC CATGGCCACC AAATCCTCCC CCCCTACCCA
-+ ATTTACCCCC TAACCCTTTT CCCCTTACCC CACGGTCACC AAATCCCCCC CTTTCACCCA
-+ GCCCACCCTT CAACCCCCCC CCTTCCGTTT TACGGCTACC AAATCCCCCC CTTTCACCCA
-+
-+ ACCCCAACCA ACCCTCCCAA AAAAACCAAA CCCAAACCCA CCGCCCAACC AA
-+ ACCCCAACCA ACCCCCCCAA AAAAACCAAA TTTAAACCCA AAACCCCCCC AA
-+ ATCCCGGTTG GCCCCCCCAA AAAAACCAAA TTTAAACCCA AAACCCCCCC AA
-+ ACCCCAATTA ACCCTTTCAA AAAAACCAAA TTTGGGCCCC AAACCCCCCC AA
Added: trunk/packages/fastdnaml/trunk/debian/tests/Makefile
===================================================================
--- trunk/packages/fastdnaml/trunk/debian/tests/Makefile (rev 0)
+++ trunk/packages/fastdnaml/trunk/debian/tests/Makefile 2008-07-06 01:11:53 UTC (rev 2154)
@@ -0,0 +1,22 @@
+# Samples and tests by Catherine Letondal <letondal at pasteur.fr>
+
+
+test: fastDNAml fastDNAml_boot
+
+oldfastDNAml:
+ cat fastdnaml.data | fastDNAml-util frequencies | fastDNAml-util printdata | fastDNAml-util treefile | fastDNAml > fastdnaml.out ; fastDNAml-util clean_checkpoints
+
+fastDNAml:
+ cat fastdnaml.data | fastDNAml-util printdata | fastDNAml > fastdnaml.out ; fastDNAml-util clean_checkpoints
+
+fastDNAml_boot:
+ cat fastdnaml.data | fastDNAml-util printdata > fastdnaml.data.tmp; fastDNAml-util fastDNAml_boot -out -boots 2 -max 2 fastdnaml.data.tmp 2
+
+clean:
+ rm -f *.tmp*
+ rm -f *.out
+ rm -f treefile*
+ rm -f checkpoint.*
+
+
+
Added: trunk/packages/fastdnaml/trunk/debian/tests/fastdnaml.data
===================================================================
--- trunk/packages/fastdnaml/trunk/debian/tests/fastdnaml.data (rev 0)
+++ trunk/packages/fastdnaml/trunk/debian/tests/fastdnaml.data 2008-07-06 01:11:53 UTC (rev 2154)
@@ -0,0 +1,20 @@
+ 4 232
+Bovine CCAAAAACCC CTTGTCCCCC CTCCCCTTTA AAACCCCCAA AAAACCCTTA AACCCCAAAA
+Mouse CCAAAAAAAA AAAACTCCAA AACCCCCCCA CCCCCCCCTA AGGTCCCCCA AACCCAGGGG
+Gorilla CCCCAAATTT TTTATCATAA AACCCCCCCA AAACCCCCCA ACCCAAACCA AACCCTTTTT
+Human CCCCAAACCC TCCACCATCC AACCCCCCCA AAACTTTTCA ACCTAAACCA AATTTTTTTT
+
+ AATAACACCC ACTACCCAAA AAAATATTCC CAAACACTCC AAAAAATACC CCCCCAACCC
+ AATAATACCC CCAACCCAAA AAAACAAACC TAAATACCTC AAAAAACACC CCCCCAATCC
+ GACCCCCCCC CTCGCCCGGA AAAACAAATT CAAACACCTC AAAAAACACC CCTTCAGCTC
+ AACCCTCCCC CCAACCCGGA AAGGCAAATT CAAACACCTC AAAGGGCACC CCTCCAACCC
+
+ GCCCACCCCC CAACCCCCCC CCCCTTGCCC CACGGTCACC CAACCCCTTT CTTTCACCCA
+ ACCCGCCCCC CAACCCCTTT TTCCCCGCCC CATGGCCACC AAATCCTCCC CCCCTACCCA
+ ATTTACCCCC TAACCCTTTT CCCCTTACCC CACGGTCACC AAATCCCCCC CTTTCACCCA
+ GCCCACCCTT CAACCCCCCC CCTTCCGTTT TACGGCTACC AAATCCCCCC CTTTCACCCA
+
+ ACCCCAACCA ACCCTCCCAA AAAAACCAAA CCCAAACCCA CCGCCCAACC AA
+ ACCCCAACCA ACCCCCCCAA AAAAACCAAA TTTAAACCCA AAACCCCCCC AA
+ ATCCCGGTTG GCCCCCCCAA AAAAACCAAA TTTAAACCCA AAACCCCCCC AA
+ ACCCCAATTA ACCCTTTCAA AAAAACCAAA TTTGGGCCCC AAACCCCCCC AA
Added: trunk/packages/fastdnaml/trunk/fastDNAml-util
===================================================================
--- trunk/packages/fastdnaml/trunk/fastDNAml-util (rev 0)
+++ trunk/packages/fastdnaml/trunk/fastDNAml-util 2008-07-06 01:11:53 UTC (rev 2154)
@@ -0,0 +1,24 @@
+#!/bin/sh
+
+BINDIR=/usr/lib/fastdnaml/bin
+
+if [ $# -lt 1 ] ; then
+ echo "Usage: $0 <utility>" 1>&2
+ echo " Existing utilities are:"
+ ls ${BINDIR}
+ exit 1
+fi
+
+WRAPPER=$0
+PROGRAM=$1
+shift
+ARGS=$*
+
+if [ -x ${BINDIR}/${PROGRAM} ]; then
+ exec ${BINDIR}/${PROGRAM} ${ARGS}
+else
+ echo "Usage: utility ${PROGRAM} does not exist in fastDNAml"
+ echo " Existing utilities are:"
+ ls ${BINDIR}
+ exit 1
+fi
Added: trunk/packages/fastdnaml/trunk/fastdnaml-1.2.1.announce
===================================================================
--- trunk/packages/fastdnaml/trunk/fastdnaml-1.2.1.announce (rev 0)
+++ trunk/packages/fastdnaml/trunk/fastdnaml-1.2.1.announce 2008-07-06 01:11:53 UTC (rev 2154)
@@ -0,0 +1,4 @@
+Warning: fastDNAml 1.2 changed drastically its user interface. Many utilities
+like "frequencies" are no longer necessary. Many default options changed.
+See the documentation or the Makefile in the tests directory.
+
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